5ED1

Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from S. cerevisiae BDF2 gene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity.

Matthews, M.M.Thomas, J.M.Zheng, Y.Tran, K.Phelps, K.J.Scott, A.I.Havel, J.Fisher, A.J.Beal, P.A.

(2016) Nat.Struct.Mol.Biol. 23: 426-433

  • DOI: 10.1038/nsmb.3203
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editin ...

    Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editing-site selectivity, and the effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. Here we describe four crystal structures of the human ADAR2 deaminase domain bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis of the ADAR deaminase domain's dsRNA specificity, its base-flipping mechanism, and its nearest-neighbor preferences. In addition, we identified an ADAR2-specific RNA-binding loop near the enzyme active site, thus rationalizing differences in selectivity observed between different ADARs. Finally, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.


    Organizational Affiliation

    Department of Chemistry, University of California, Davis, Davis, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Double-stranded RNA-specific editase 1
A, D
403Homo sapiensMutation(s): 1 
Gene Names: ADARB1 (ADAR2, DRADA2, RED1)
EC: 3.5.4.37
Find proteins for P78563 (Homo sapiens)
Go to Gene View: ADARB1
Go to UniProtKB:  P78563
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3')B23Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3')C23Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IHP
Query on IHP

Download SDF File 
Download CCD File 
A, D
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
8AZ
Query on 8AZ
B
RNA linkingC9 H14 N5 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.362α = 90.00
b = 107.498β = 90.00
c = 121.097γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM061115

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2016-05-18
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Derived calculations